ImageJ Ops

<!DOCTYPE html> <html> <head> <title>ImageJ Ops</title> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=3" /> <meta content="ImageJ Wiki" property="og:site_name"> <meta content="ImageJ Ops" property="og:title"> <meta content="article" property="og:type"> <meta content="The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others." property="og:description"> <meta content="https://imagej.github.io/libs/imagej-ops/index" property="og:url"> <meta content="https://imagej.github.io/media/icons/imagej2.png" property="og:image"> <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png"> <link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png"> <link 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Click the logo for details.</span></span></a> <h1>ImageJ Ops</h1> <span class="project-counterweight"> </span> </header> </div>   <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> <div class="notice" style="font-size: 2; background: #ebf2f8; border-left: 10px solid #67a1fe"><div class="notice-icon"><img src="/media/icons/info.svg" width="32"></div><div class="notice-content"><p>The content of this page has not been vetted since shifting away from MediaWiki. If you’d like to help, check out the <a href="/events/wiki-grand-opening/how-to-help">how to help guide</a>!</p> </div> </div> <p>ImageJ Ops is a framework for reusable image processing operations. Ops extends Java’s mantra of “write once, run anywhere” to image processing algorithms.</p> <p>The central goal is to enable programmers to code an image processing algorithm in the Ops framework, which is then usable as-is from any <a href="/libs/scijava">SciJava</a>-compatible software project, such as <a href="/software/imagej2">ImageJ2</a>, <a href="/software/cellprofiler">CellProfiler</a>, <a href="/software/knime">KNIME</a>, <a href="/software/omero">OMERO</a> and <a href="/software/alida">Alida</a>.</p> <h2 id="design-goals">Design goals</h2> <p>Ops has three major design goals:</p> <ol> <li><strong>Easy to use and extend.</strong> There must be a wealth of easy-to-use image processing operations (“ops”), as well as an easy framework for extending those ops in new directions.</li> <li><strong>Powerful and general.</strong> An op should be able to consist of any number of typed input and output parameters, operating on arbitrary data structures, including images of N dimensions stored in a myriad of different ways: as files on disk, programmatically generated in memory, or in remote databases. Using the powerful <a href="/libs/imglib2">ImgLib2</a> library achieves this ambitious goal.</li> <li><strong>Very fast.</strong> Even though ImgLib2 is vastly more general than ImageJ’s data model, that generality should not come at the expense of performance. Otherwise, users must pay a time tax to do the same things they could already do in ImageJ. The ImageJ Ops framework needs to provide a means to override <em>any</em> general-but-slow op with a faster-but-more-specific alternative, fully transparently to the user.</li> </ol> <h2 id="getting-started">Getting started</h2> <p>Start by reading these Jupyter notebooks:</p> <ul> <li><a href="https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb">Using ImageJ Ops</a> - to call ops from your scripts.</li> <li><a href="https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/2-Ops.ipynb">Extending ImageJ: Ops</a> - to write your own ops.</li> </ul> <p>Ops are a special type of ImageJ plugin, so a basic understanding of the <a href="/develop/plugins">SciJava plugin framework</a> is strongly recommended.</p> <p>In addition to cloning the <a href="https://github.com/imagej/imagej-ops">imagej-ops</a> itself, the following components have useful Ops examples:</p> <ul> <li><a href="https://github.com/imagej/imagej-tutorials/">ImageJ-tutorials</a> - examples of ImageJ plugins using Ops</li> <li><a href="https://github.com/imagej/imagej-scripting/">ImageJ-scripting</a> - provides <a href="/scripting/templates">templates in the Script Editor</a></li> </ul> <h2 id="tutorials-and-workshops">Tutorials and workshops</h2> <ul> <li><a href="/develop/writing-ops">Step-by-step guide: Adding new ops</a></li> <li><a href="https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/1-Using-ImageJ/2-ImageJ-Ops.ipynb">ImageJ Tutorial: Introduction to ImageJ Ops</a></li> <li><a href="https://nbviewer.jupyter.org/github/imagej/tutorials/blob/master/notebooks/2-Extending-ImageJ/2-Ops.ipynb">Extending ImageJ: Ops</a></li> <li>“Scripting in ImageJ - An introduction to ImageJ Ops” (February 2017 NEUBIAS2020) – <a href="/presentations/2017-02-12-imagej-ops-neubias/#/">slides</a></li> <li>“ImageJ2 scripts: Parameters + ImageJ Ops” (ImageJ conference 2015) – <a href="/presentations/2015-09-04-imagej2-scripting/">slides</a>, <a href="https://vimeo.com/140098817">video 1</a>, <a href="https://vimeo.com/140098835">video 2</a></li> <li>“The ImageJ Ops Framework: Image processing made easy” (January 2015) – <a href="/presentations/2015-01-12-imagej-ops/">slides</a></li> <li>“Intro to ImageJ Ops - Usage and Development” (November 2015) – <a href="http://workshops.imagej.net/IntroToOps.pdf">slides</a></li> </ul> <h2 id="faq">FAQ</h2> <h3 id="why-not-implement-algorithms-as-plain-old-java-methods">Why not implement algorithms as “plain old Java” methods?</h3> <p>The Ops matching framework provides <strong>extensibility.</strong> Ops are plugins, so any developer can override the behavior of a particular op as needed—e.g., for improved performance of a special case. See “Design goals” above.</p> <h3 id="can-a-cc-or-matlab-function-be-converted-to-an-op">Can a C/C++ or MATLAB function be converted to an op?</h3> <p>Yes, but there is no automagic wrapping of native/external functionality in Ops. The <a href="https://github.com/imagej/ops-experiments">ops-experiments</a> project is an ongoing effort to work out a maven based build system for ops that use native code. The efforts so far have focused on wrapping, cuda, mkl and tensorflow implementations of deconvolution algorithms using <a href="https://github.com/bytedeco/javacpp">javacpp</a>.</p> <h3 id="is-there-a-list-of-ops-somewhere-with-brief-descriptions-of-their-functionalities">Is there a list of Ops somewhere with brief descriptions of their functionalities?</h3> <p>For an interactive tool to see all available Ops, see the <a href="/plugins/op-finder">Op Finder</a> documentation.</p> <p>For the core Ops available, you can go to the <a href="https://javadoc.scijava.org/ImageJ/?net/imagej/ops/package-summary.html">ImageJ Ops</a> javadocs. Any class under the package <code class="language-plaintext highlighter-rouge">net.imagej.ops</code> is related to Ops.</p> <p>You can also use the <a href="/scripting/script-editor">Script Editor</a> in ImageJ and actively search using Ops itself. For example in groovy language:</p> <figure class="highlight"><pre><code class="language-groovy" data-lang="groovy"><span class="c1">// @OpService ops</span> <span class="n">print</span> <span class="n">ops</span><span class="o">.</span><span class="na">help</span><span class="o">()</span></code></pre></figure> <p>in groovy will give a list of every Op signature. The <code class="language-plaintext highlighter-rouge">help</code> op can also provide information about ops or namespaces; e.g., <code class="language-plaintext highlighter-rouge">ops.help("add")</code> will return info about available <code class="language-plaintext highlighter-rouge">add</code> ops.</p> <h3 id="are-there-any-ops-for-image-processing">Are there any Ops for image processing?</h3> <p>Yes, there are. Take a look at the existing ops using the <a href="#is-there-a-list-of-ops-somewhere-with-brief-descriptions-of-their-functionalities"> Ops Browser</a> or the <code class="language-plaintext highlighter-rouge">net.imagej.ops.*</code> packages in the <a href="http://javadoc.imagej.net/ImageJ/">ImageJ javadocs</a>.</p> <h3 id="what-are-the-ops-that-need-to-be-developed-in-the-future">What are the Ops that need to be developed in the future?</h3> <p>Ops is under development at the moment, as indicated by the 0.x.x version number. For ideas and discussions of future developments visit the <a href="https://github.com/imagej/imagej-ops/">ImageJ Ops GitHub page</a> and take a look at the issues and pull requests.</p> <h3 id="why-is-matching-important">Why is matching important?</h3> <p>This is a necessary part of any plugin-based infrastructure (see <a href="https://en.wikipedia.org/wiki/Inversion_of_control">Inversion of control</a>). The core library (ImageJ Ops) has many built-in operations, but:</p> <ol> <li>cannot possibly cover all possible implementations and</li> <li>would be impractical if a user had to explicitly call the precise signature for their arguments.</li> </ol> <p>Ops matching is an additional layer that allows plugin selection to be tailored to the arguments of the function being called.</p> <p>A contrived example: Suppose the default ops implementation of <code class="language-plaintext highlighter-rouge">add(array, array)</code> iterates over the arrays and combines their values.</p> <p>Then guava comes up with a way to combine arrays that is 100x faster; we do not want a guava dependency in the base ops library, but we can have an “imagej-ops-guava” component that provides a <code class="language-plaintext highlighter-rouge">GuavaAddArrayOp</code>.</p> <p>Then an independent developer comes up with a new way to add the arrays that’s 50,000x faster. They turn it into a closed-source, proprietary Op and sell it.</p> <p>Regardless of this proliferation of implementations, a user just has to write <code class="language-plaintext highlighter-rouge">ops.math().add(array1, array2)</code> and it will work. If they have the guava implementation on their classpath it will be faster, and if they purchase the proprietary implementation it will be faster still. 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